Eukaryotic genomes are packaged into nucleosomes whose position and
chemical modification state can profoundly influence regulation of gene
expression. We profiled nucleosome modifications across the yeast genome
using chromatin immunoprecipitation coupled with DNA microarrays to
produce high-resolution genome-wide maps of histone acetylation and
methylation. These maps take into account changes in nucleosome occupancy
at actively transcribed genes, and in doing so, revise previous assessments
of the modifications associated with gene expression. Both acetylation
and methylation of histones are associated with transcriptional activity,
but the former occurs predominantly at the beginning of genes whereas
the latter can occur throughout transcribed regions. Most notably, specific
methylation events are associated with the beginning, middle and end
of actively transcribed genes. These maps provide the foundation for
further understanding the roles of chromatin in gene expression and
genome maintenance.